Double vertices while Retopologizing
It's difficult to tell without more information, but it looks like you just have a broken mesh.  

Simply select the two vertices and press Alt + M to merge them together to create a quad:







EDIT: As far as closing up the back seam...

Just create Tris on the bottom by selecting three vertices and pressing F to fill.

With the Merge Vertices option enabled, it will automatically connect both sides of the Mirror Modifier:



You can Ctrl + RightClick to select a series of vertices at the seam and just pull them over to connect since you've enabled Merge.